On Tue, Apr 3, 2018 at 9:12 AM, Stefano Zampini <[email protected]> wrote:
> > On Apr 3, 2018, at 4:58 PM, Satish Balay <[email protected]> wrote: > > On Tue, 3 Apr 2018, Kong, Fande wrote: > > On Tue, Apr 3, 2018 at 1:17 AM, Smith, Barry F. <[email protected]> > wrote: > > > Each external package definitely needs its own duplicated communicator; > cannot share between packages. > > The only problem with the dups below is if they are in a loop and get > called many times. > > > > The "standard test" that has this issue actually has 1K fields. MOOSE > creates its own field-split preconditioner (not based on the PETSc > fieldsplit), and each filed is associated with one PC HYPRE. If PETSc > duplicates communicators, we should easily reach the limit 2048. > > I also want to confirm what extra communicators are introduced in the bad > commit. > > > To me it looks like there is 1 extra comm created [for MATHYPRE] for each > PCHYPRE that is created [which also creates one comm for this object]. > > > You’re right; however, it was the same before the commit. > I don’t understand how this specific commit is related with this issue, > being the error not in the MPI_Comm_Dup which is inside MatCreate_MATHYPRE. > Actually, the error comes from MPI_Comm_create > > > > > > * frame #5: 0x00000001068defd4 libmpi.12.dylib`MPI_Comm_create + > 3492 frame #6: 0x00000001061345d9 > libpetsc.3.07.dylib`hypre_GenerateSubComm(comm=-1006627852, > participate=<unavailable>, new_comm_ptr=<unavailable>) + 409 at > gen_redcs_mat.c:531 [opt] frame #7: 0x000000010618f8ba > libpetsc.3.07.dylib`hypre_GaussElimSetup(amg_data=0x00007fe7ff857a00, > level=<unavailable>, relax_type=9) + 74 at par_relax.c:4209 [opt] frame > #8: 0x0000000106140e93 > libpetsc.3.07.dylib`hypre_BoomerAMGSetup(amg_vdata=<unavailable>, > A=0x00007fe80842aff0, f=0x00007fe80842a980, u=0x00007fe80842a510) + 17699 > at par_amg_setup.c:2108 [opt] frame #9: 0x0000000105ec773c > libpetsc.3.07.dylib`PCSetUp_HYPRE(pc=<unavailable>) + 2540 at hypre.c:226 > [opt* > > How did you perform the bisection? make clean + make all ? Which version > of HYPRE are you using? > I did more aggressively. "rm -rf arch-darwin-c-opt-bisect " "./configure --optionsModule=config.compilerOptions -with-debugging=no --with-shared-libraries=1 --with-mpi=1 --download-fblaslapack=1 --download-metis=1 --download-parmetis=1 --download-superlu_dist=1 --download-hypre=1 --download-mumps=1 --download-scalapack=1 PETSC_ARCH=arch-darwin-c-opt-bisect" HYPRE verison: self.gitcommit = 'v2.11.1-55-g2ea0e43' self.download = ['git://https://github.com/LLNL/hypre',' https://github.com/LLNL/hypre/archive/'+self.gitcommit+'.tar.gz'] I do not think this is caused by HYPRE. Fande, > > But you might want to verify [by linking with mpi trace library?] > > > There are some debugging hints at https://lists.mpich.org/ > pipermail/discuss/2012-December/000148.html [wrt mpich] - which I haven't > checked.. > > Satish > > > > Fande, > > > > > To debug the hypre/duplication issue in MOOSE I would run in the > debugger with a break point in MPI_Comm_dup() and see > who keeps calling it an unreasonable amount of times. (My guess is this is > a new "feature" in hypre that they will need to fix but only debugging will > tell) > > Barry > > > On Apr 2, 2018, at 7:44 PM, Balay, Satish <[email protected]> wrote: > > We do a MPI_Comm_dup() for objects related to externalpackages. > > Looks like we added a new mat type MATHYPRE - in 3.8 that PCHYPRE is > using. Previously there was one MPI_Comm_dup() PCHYPRE - now I think > is one more for MATHYPRE - so more calls to MPI_Comm_dup in 3.8 vs 3.7 > > src/dm/impls/da/hypre/mhyp.c: ierr = MPI_Comm_dup(PetscObjectComm(( > > PetscObject)B),&(ex->hcomm));CHKERRQ(ierr); > > src/dm/impls/da/hypre/mhyp.c: ierr = MPI_Comm_dup(PetscObjectComm(( > > PetscObject)B),&(ex->hcomm));CHKERRQ(ierr); > > src/dm/impls/swarm/data_ex.c: ierr = MPI_Comm_dup(comm,&d->comm); > > CHKERRQ(ierr); > > src/ksp/pc/impls/hypre/hypre.c: ierr = MPI_Comm_dup(PetscObjectComm(( > > PetscObject)pc),&(jac->comm_hypre));CHKERRQ(ierr); > > src/ksp/pc/impls/hypre/hypre.c: ierr = MPI_Comm_dup(PetscObjectComm(( > > PetscObject)pc),&(ex->hcomm));CHKERRQ(ierr); > > src/ksp/pc/impls/hypre/hypre.c: ierr = MPI_Comm_dup(PetscObjectComm(( > > PetscObject)pc),&(ex->hcomm));CHKERRQ(ierr); > > src/ksp/pc/impls/spai/ispai.c: ierr = > > MPI_Comm_dup(PetscObjectComm((PetscObject)pc),&(ispai->comm_ > spai));CHKERRQ(ierr); > > src/mat/examples/tests/ex152.c: ierr = MPI_Comm_dup(MPI_COMM_WORLD, > > &comm);CHKERRQ(ierr); > > src/mat/impls/aij/mpi/mkl_cpardiso/mkl_cpardiso.c: ierr = > > MPI_Comm_dup(PetscObjectComm((PetscObject)A),&(mat_mkl_ > cpardiso->comm_mkl_cpardiso));CHKERRQ(ierr); > > src/mat/impls/aij/mpi/mumps/mumps.c: ierr = > > MPI_Comm_dup(PetscObjectComm((PetscObject)A),&(mumps->comm_ > mumps));CHKERRQ(ierr); > > src/mat/impls/aij/mpi/pastix/pastix.c: ierr = > > MPI_Comm_dup(PetscObjectComm((PetscObject)A),&(lu->pastix_ > comm));CHKERRQ(ierr); > > src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c: ierr = > > MPI_Comm_dup(PetscObjectComm((PetscObject)A),&(lu->comm_ > superlu));CHKERRQ(ierr); > > src/mat/impls/hypre/mhypre.c: ierr = MPI_Comm_dup(PetscObjectComm(( > > PetscObject)B),&hB->comm);CHKERRQ(ierr); > > src/mat/partition/impls/pmetis/pmetis.c: ierr = > > MPI_Comm_dup(pcomm,&comm);CHKERRQ(ierr); > > src/sys/mpiuni/mpi.c: MPI_COMM_SELF, MPI_COMM_WORLD, and a > > MPI_Comm_dup() of each of these (duplicates of duplicates return the same > communictor) > > src/sys/mpiuni/mpi.c:int MPI_Comm_dup(MPI_Comm comm,MPI_Comm *out) > src/sys/objects/pinit.c: ierr = MPI_Comm_dup(MPI_COMM_WORLD,& > > local_comm);CHKERRQ(ierr); > > src/sys/objects/pinit.c: ierr = MPI_Comm_dup(MPI_COMM_WORLD,& > > local_comm);CHKERRQ(ierr); > > src/sys/objects/tagm.c: ierr = MPI_Comm_dup(comm_in,comm_out) > > ;CHKERRQ(ierr); > > src/sys/utils/mpiu.c: ierr = MPI_Comm_dup(comm,&local_comm) > > ;CHKERRQ(ierr); > > src/ts/impls/implicit/sundials/sundials.c: ierr = > > MPI_Comm_dup(PetscObjectComm((PetscObject)ts),&(cvode->comm_ > sundials));CHKERRQ(ierr); > > > Perhaps we need a PetscCommDuplicateExternalPkg() to somehow avoid > > these MPI_Comm_dup() calls? > > > Satish > > On Tue, 3 Apr 2018, Smith, Barry F. wrote: > > > Are we sure this is a PETSc comm issue and not a hypre comm > > duplication issue > > > frame #6: 0x00000001061345d9 libpetsc.3.07.dylib`hypre_ > > GenerateSubComm(comm=-1006627852, participate=<unavailable>, > new_comm_ptr=<unavailable>) + 409 at gen_redcs_mat.c:531 [opt] > > > Looks like hypre is needed to generate subcomms, perhaps it generates > > too many? > > > Barry > > > On Apr 2, 2018, at 7:07 PM, Derek Gaston <[email protected]> wrote: > > I’m working with Fande on this and I would like to add a bit more. > > There are many circumstances where we aren’t working on COMM_WORLD at all > (e.g. working on a sub-communicator) but PETSc was initialized using > MPI_COMM_WORLD (think multi-level solves)… and we need to create > arbitrarily many PETSc vecs/mats/solvers/preconditioners and solve. We > definitely can’t rely on using PETSC_COMM_WORLD to avoid triggering > duplication. > > > Can you explain why PETSc needs to duplicate the communicator so much? > > Thanks for your help in tracking this down! > > Derek > > On Mon, Apr 2, 2018 at 5:44 PM Kong, Fande <[email protected]> wrote: > Why we do not use user-level MPI communicators directly? What are > > potential risks here? > > > > Fande, > > On Mon, Apr 2, 2018 at 5:08 PM, Satish Balay <[email protected]> > > wrote: > > PETSC_COMM_WORLD [via PetscCommDuplicate()] attempts to minimize calls > > to MPI_Comm_dup() - thus potentially avoiding such errors > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs. > > anl.gov_petsc_petsc-2Dcurrent_docs_manualpages_Sys_ > PetscCommDuplicate.html&d=DwIBAg&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB_ > _aEkJFOKJFd00&r=DUUt3SRGI0_JgtNaS3udV68GRkgV4ts7XKfj2opmi > CY&m=jgv7gpZ3K52d_FWMgkK9yEScbLA7pkrWydFuJnYflsU&s=_ > zpWRcyk3kHuEHoq02NDqYExnXIohXpNnjyabYnnDjU&e= > > > > Satish > > On Mon, 2 Apr 2018, Kong, Fande wrote: > > On Mon, Apr 2, 2018 at 4:23 PM, Satish Balay <[email protected]> > > wrote: > > > Does this 'standard test' use MPI_COMM_WORLD' to crate PETSc objects? > > If so - you could try changing to PETSC_COMM_WORLD > > > > I do not think we are using PETSC_COMM_WORLD when creating PETSc > > objects. > > Why we can not use MPI_COMM_WORLD? > > > Fande, > > > > Satish > > > On Mon, 2 Apr 2018, Kong, Fande wrote: > > Hi All, > > I am trying to upgrade PETSc from 3.7.6 to 3.8.3 for MOOSE and its > applications. I have a error message for a standard test: > > > > > > > > > > *preconditioners/pbp.lots_of_variables: MPI had an > errorpreconditioners/pbp.lots_of_variables: > ------------------------------------------------ > > preconditioners/pbp.lots_of_variables: > > Other MPI error, error stack:preconditioners/pbp.lots_of_variables: > PMPI_Comm_dup(177)..................: MPI_Comm_dup(comm=0x84000001, > new_comm=0x97d1068) failedpreconditioners/pbp.lots_of_variables: > PMPI_Comm_dup(162)..................: > preconditioners/pbp.lots_of_variables: > MPIR_Comm_dup_impl(57)..............: > preconditioners/pbp.lots_of_variables: > MPIR_Comm_copy(739).................: > preconditioners/pbp.lots_of_variables: > MPIR_Get_contextid_sparse_group(614): Too many communicators > > (0/2048 > > free > > on this process; ignore_id=0)* > > > I did "git bisect', and the following commit introduces this issue: > > > > > > > > > *commit 49a781f5cee36db85e8d5b951eec29f10ac13593Author: Stefano > > Zampini > > <[email protected] <[email protected]>>Date: Sat > > Nov 5 > > 20:15:19 2016 +0300 PCHYPRE: use internal Mat of type MatHYPRE > hpmat already stores two HYPRE vectors* > > Before I debug line-by-line, anyone has a clue on this? > > > Fande, > > > > > > > > > >
